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After testing #464 which gave me errors, I noticed that I wasn't able to reinstall ADS. After the pip install and venv activation, I get this whenever I try to run one of the CLI scripts:
Error:
…
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When running `sct_run_batch`, user points to a dataset. The log file indicates the dataset that was used, e.g.:
~~~
sct_run_batch arguments were:
batch_log: sct_run_batch_log.txt
config: /home/jco…
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The CLI tests for our `default_SEM` are covered by AxonDeepSeg. However, our `default_TEM model` is not tested by the CLI see [here](https://github.com/neuropoly/axondeepseg/blob/3bcc87d29816d881dcc4b…
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Working branch on git-annex: `jca/update-groundtruth`.
P091 and P167 do not have manual MS lesion segmentation file. They should exist (even if they are empty).
# Batch commands
Run in folder…
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**Description**
While doing some refactoring for the latest features, we missed something for model native resolution.
**To Reproduce**
For a model without a `Resample` transformation:
```
2022…
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Due to some recent changes (e.g. [renaming the config key "weighted_cost_activate" to "weighted_cost-activate" in train_model.py](https://github.com/neuropoly/axondeepseg/blame/150cf46c8e8326f1ebbc4bd…
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Following the release of version 4, the models were updated on their respective repos:
https://github.com/axondeepseg/default-SEM-model
https://github.com/axondeepseg/default-TEM-model
https://gith…
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## This issue is placed in order to start a discussion about the potential options.
The datasets that we have in our disposal are only getting bigger.
We should slowly start thinking how we ca…
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In order to run axondeepseg and ivadomed in the same environment, we would need to upgrade the following requirements:
`pillow==6.2.0` to at least `==7.0.0`
`scikit-learn==0.19.2` to at least `==0…
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I'm trying to use train_model with providing initial weights, but I'm having several issues.
- The first one: IOError: [Errno 2] No such file or directory: '/Users/oubou_admin/axondeepseg/AxonDeep…